neurospaces 0.1675 Thu, 27 Dec 2007 15:58:18 -0600 hugo

Index of group ./specifications/sli

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running GENESIS 2 scripts and importing their models

1. Exploring the GENESIS 2 backward compatibility library

2. Running a GENESIS 2 script

3. Loading a model that is coded inside a GENESIS 2 script without running the simulation in the script

1. Exploring the GENESIS 2 backward compatibility library

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

Comments, Preparation, Reparation

1. Comment for this test definition

Likely this test needs to be reworked a little bit because some features of the backward compatibility module are still under development.

1.1. Can we show the root of the library with the backward compatibility scripts?

1. Executed command	library_show sli
2. Expected output	PurkM9_model

1.2. Can we show the purkinje cell model subdirectory of the library with the backward compatibility scripts?

1. Executed command

library_show sli PurkM9_model

2. Expected output


    - ACTIVE-main1.g
    - ACTIVE-soma1.g
    - CLIMB9.g
    - CLIMBSPINE9.g
    - CURRENT9.g
    - ISPINE9.g
    - PASSIVE9-current.g
    - PASSIVE9-current1.g
    - PASSIVE9-current2.g
    - Purk2M0.p
    - Purk2M0s.p
    - Purk2M0sA.p
    - Purk2M9.p
    - Purk2M9_main1.p
    - Purk2M9_soma.p
    - Purk2M9s.p
    - Purk2M9s1.p
    - Purk2M9s10.p
    - Purk2M9s14.p
    - Purk2M9s19.p
    - Purk2M9s2.p
    - Purk2M9s25.p
    - Purk2M9s29.p
    - Purk2M9s3.p
    - Purk2M9s37.p
    - Purk2M9s4.p
    - Purk2M9s44.p
    - Purk2M9s45.p
    - Purk2M9s6.p
    - Purk2M9s8b.p
    - Purk2M9sA.p
    - Purk_chan.g
    - Purk_chanload.g
    - Purk_chansave.g
    - Purk_cicomp.g
    - Purk_cicomp_passive.g
    - Purk_comp.g
    - Purk_const.g
    - Purk_icomp.g
    - Purk_spicomp.g
    - Purk_syn.g
    - SYNCHRONORM9.g
    - SYNCHROPASS9.g
    - VIVO.g
    - defaults.g
    - purkinje_simplifying.g
    - schedule.g

2. Running a GENESIS 2 script

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

Comments, Preparation, Reparation

1. Comment for this test definition	This test uses the original scripts of the Purkinje cell model
2. Preparation needed before the commands below :	Create the results directory
3. And repared afterwards using :	Remove the generated output files in the results directory

2.1. Can we run the current injection script?

1. Executed command	sli_run /usr/local/ns-sli/tests/scripts/PurkM9_model/CURRENT9.g
2. Expected output

2.2. Can the morphology be read (1)?

1. Expected output

tests/scripts/PurkM9_model/Purk2M9.p read: 1600 compartments

2.3. Can we query the resulting model using the querymachine: total volume ?

1. Executed command	printparameter /Purkinje TOTALVOLUME
2. Expected output	value = 5.37774e-14

2.4. Can we query the resulting model using the querymachine: total surface ?

1. Executed command

printparameter /Purkinje TOTALSURFACE

2. Expected output

value = 2.60908e-07

3. Comment

even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.  This value changed from value = 2.61092e-07 to 2.60908e-07 after float to double accommodations in the model-container.

2.5. Can we query the resulting model using the querymachine: segment count ?

1. Executed command	segmentcount /Purkinje
2. Expected output	Number of segments : 1600

2.6. quit the querymachine

1. Executed command	quit
2. Expected output

2.7. Do we see the simulation time after the simulation has finished ?

1. Expected output

time = 0.500060 ; step = 25003

2.8. What is the contents of the current directory ?

1. Executed command	sh ls -lastr
2. Expected output	results

2.9. What is the contents of the results directory ?

1. Executed command	sh ls -lastr results
2. Expected output	PurkM9

2.10. quit the simulator

1. Executed command	quit
2. Expected output

2.11. Is the generated output correct (1)?

1. Expected output

application_output_file: results/PurkM9_soma_1.5nA
expected_output_file: /usr/local/ns-sli/tests/specifications/strings/PurkM9_soma_1.5nA.g3-double

2. Comment

The output file is taken from the ns-sli installation.

3. Loading a model that is coded inside a GENESIS 2 script without running the simulation in the script

Startup command : bin/genesis-g3

(No model has been loaded for the following set of commands.)

Comments, Preparation, Reparation

1. Comment for this test definition

This test uses the original scripts of the Purkinje cell model

3.1. Can we load the model of the current injection script into the model container without running the simulation?

1. Executed command	sli_load /usr/local/ns-sli/tests/scripts/PurkM9_model/CURRENT9.g
2. Expected output

3.2. Can the morphology be read (2)?

1. Expected output

tests/scripts/PurkM9_model/Purk2M9.p read: 1600 compartments

3.3. Can we query the resulting model using the querymachine: total volume ?

1. Executed command	printparameter /Purkinje TOTALVOLUME
2. Expected output	value = 5.37774e-14

3.4. Can we query the resulting model using the querymachine: total surface ?

1. Executed command

printparameter /Purkinje TOTALSURFACE

2. Expected output

value = 2.60908e-07

3. Comment

even without spines, this value is very different from the value in table 2 of the Rapp paper, this is due to shrinkage correction, yet there is an unexplained anomaly in the difference for surface and volume.  This value changed from value = 2.61092e-07 to 2.60908e-07 after float to double accommodations in the model-container.

3.5. Can we query the resulting model using the querymachine: segment count ?

1. Executed command	segmentcount /Purkinje
2. Expected output	Number of segments : 1600

3.6. quit the querymachine

1. Executed command	quit
2. Expected output
3. Comment	without the wait command, the quit command is not executed, dont know why

3.7. Do we see the simulation time after the simulation has finished ?

1. Expected output	time = 0.500060 ; step = 25003
2. This test is currently not executed	(disabled is 'the sli_load command prevents the simulation from being run')

3.8. quit the simulator

1. Executed command	quit
2. Expected output
3. This test is currently not executed	(disabled is 'this test is here to make sure the output is flushed, but the test for the output is disabled.')

3.9. Is the generated output correct (2)?

1. Expected output

application_output_file: ./..//results/PurkM9_soma_1.5nA
expected_output_file: /usr/local/ns-sli/tests/specifications/strings/PurkM9_soma_1.5nA.g3-double

2. Comment

The output file is taken from the ns-sli installation.

3. This test is currently not executed

(disabled is 'the sli_load command prevents the simulation from being run, so no output has been produced')

3.10. Can we export a channel of the model to NDF format?

1. Executed command

ndf_save /Purkinje/soma/NaF/** STDOUT

2. Expected output

#!neurospacesparse
// -*- NEUROSPACES -*-

NEUROSPACES NDF

IMPORT
END IMPORT

PRIVATE_MODELS
END PRIVATE_MODELS

PUBLIC_MODELS
  ALIAS "Purk_NaF" "NaF"
    BINDINGS
      INPUT ..-&gt;Vm,
    END BINDINGS
    PARAMETERS
      PARAMETER ( G_MAX = 74999.9 ),
    END PARAMETERS
  END ALIAS
END PUBLIC_MODELS

3. This test is currently not executed

(disabled is 'since I mapped ndf_save to library export mode, it now produces to verbose output, working on it')

3.11. Can we export a channel of the model to XML format?

1. Executed command

xml_save /Purkinje/soma/NaF/** STDOUT

2. Expected output

&lt;import&gt;
&lt;/import&gt;

&lt;private_models&gt;
&lt;/private_models&gt;

&lt;public_models&gt;
  &lt;alias&gt; &lt;prototype&gt;Purk_NaF&lt;/prototype&gt; &lt;name&gt;NaF&lt;/name&gt;
    &lt;bindings&gt;
      &lt;input&gt; &lt;name&gt;..-&gt;Vm&lt;/name&gt; &lt;/input&gt;
    &lt;/bindings&gt;
    &lt;parameters&gt;
      &lt;parameter&gt; &lt;name&gt;G_MAX&lt;/name&gt;&lt;value&gt;74999.9&lt;/value&gt; &lt;/parameter&gt;
    &lt;/parameters&gt;
  &lt;/alias&gt;
&lt;/public_models&gt;

3. This test is currently not executed

(disabled is 'since I mapped ndf_save to library export mode, it now produces to verbose output, working on it')